sorry if this has already been covered but if you have a rare stone for a pet breed or any breed and it raises it to rare, with the stats does it increase those stats to a rare and if so what is the rare strength of the pet versus a rare that you find in the wild? would it be better in the long run to wait for a rare of just a common pet and rare up the ultra hard to get pets?

The stats increase, and it's just as strong as a rare wild pet. If you use a stone on a wild pet, it will be exactly as if you caught the rare version -- it will even lose 1-2 levels as though it were just captured.